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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 24/09/2026

Tutorial created by Razan Abbara. Thanks to the metrics developers @rolanddunbrack.bsky.social, Arne Elofsson, and @ahramkim.bsky.social, and EBI and GoogleDeepmind members; Sameer Velankar, @jen-fleming.bsky.social, @olegkovalevskiy.bsky.social, Melanie Vollmar and @jellaway.bsky.social.

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 24/09/2026

How do pLDDT, ipTM, ipSAE, pDockQ2 and LIS fit together? See how these metrics work together to assess confidence in an AlphaFold DB complex interface. 🎬 Watch the full tutorial: youtu.be/k4yBqddtPyQ #AlphaFold #AlphaFoldDB

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 23/09/2026

It’s been so exciting to work together on this as part of the MDDB project! A big thank you to our partners: @irbbarcelona.org , BSC-CNS, University of Oxford, Nostrum Biodiscovery, EPFL

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 23/09/2026

📢 New in PDBe-KB! Explore MD simulation annotations in ProtVista: residue exposure from MDposit and membrane interactions from MemProtMD. PDBe and PDBe-KB pages also link to simulations in MDposit. 🔗 www.ebi.ac.uk/pdbe/pdbe-kb...

PDBe and PDBe-KB now incorporate annotations from molecular dynamics simulations.
New feature.
MDDB-PDBe integration.

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 21/09/2026

Tutorial created by Razan Abbara. Thanks to the metrics developers @rolanddunbrack.bsky.social, Arne Elofsson, @ahramkim.bsky.social, and EBI and GoogleDeepmind members; Sameer Velankar, @jen-fleming.bsky.social, @olegkovalevskiy.bsky.social, Melanie Vollmar and @jellaway.bsky.social

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 21/09/2026

A predicted interaction may involve only a small region of a protein complex. How can we identify confidence in that local interface when the surrounding regions have high PAE? Our tutorial uses a PAE matrix to explain how LIS can help 👇 youtu.be/k4yBqddtPyQ #AlphaFold #AlphaFoldDB

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 10/09/2026

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 10/09/2026

Same predicted complex, different confidence scores: ipTM: 0.38 ipSAE: 0.75 Why can these metrics differ? Full breakdown 👇 youtu.be/k4yBqddtPyQ #AlphaFold #AFDB

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 04/09/2026

Thanks to the metrics developers @rolanddunbrack.bsky.social, Arne Elofsson, @ahramkim.bsky.social for their contribution to reviewing this tutorial, and EBI and GoogleDeepmind members; Sameer Velankar, @jen-fleming.bsky.social, @olegkovalevskiy.bsky.social, Melanie Vollmar and @jellaway.bsky.social

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 03/09/2026

New video 🎥 The AlphaFold-Multimer prediction for your protein looks great. But how confident should you actually be in it? Razan Abbara breaks down the 5 confidence metrics behind every AFDB multimer entry: pLDDT · ipTM · ipSAE · pDockQ2 · LIS 👇 youtu.be/k4yBqddtPyQ #AlphaFold #AFDB

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 25/08/2026

🚀 New updates improve metalloprotein data across the PDB Archive. ~15,500 PDB entries and ~900 metal-containing CCDs now feature more complete chemical descriptions and metal coordination annotations. ⬇️More ⬇️ www.wwpdb.org/news/news?ye... #PDB

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 18/08/2026

🚨Get ready for the future of the PDB Archive! A new publication describes the PDB Beta Archive to support PDB users as they transition to the extended PDB ID and PDBx/mmCIF format. Start preparing for the July 21, 2027 transition. 📄Read here: journals.iucr.org/d/issues/202... #PDB

journals.iucr.org

Protein Data Bank (PDB) Archive: a new architecture (beta) for scalable, PDBx/mmCIF-based data distribution

wwPDB has extended PDB IDs to 12 characters with a prefix `pdb_' followed by eight alphanumeric characters in lower case (for example pdb_1000axyz). A beta version of the PDB Archive (https://files-be...

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 17/08/2026

🌟Use Shortlinks to Transition to the PDB Beta Archive Shortlinks make it easier to download data using extended PDB IDs without coding specific file paths. Start using shortlinks today ahead of the July 21, 2027 transition. ⬇️More ⬇️ www.wwpdb.org/news/news?ye... #PDB

wwpdb.org

Use Shortlinks to Transition to the PDB Beta Archive

wwPDB: Worldwide Protein Data Bank

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Reposted by Protein Data Bank in Europe (PDBe)

Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 23/06/2026

🤖 Want to use AI and LLMs to unlock molecular dynamics data? Join #PDBe at #EMBLEBI and help build next-gen MD data integration across PDBe, UniProt, AlphaFoldDB and more. 🌎 Apply from anywhere 🔗 embl.wd103.myworkdayjobs.com/EMBL/job/Hin... #AI #StructuralBiology #Database

embl.wd103.myworkdayjobs.com

Bioinformatician

About the team We are seeking a Bioinformatician with expertise in data integration and experience in structural biology and molecular dynamics (MD) data to join the Velankar team at the European Bioi...

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 12/08/2026

📄New recommendations for fragment-screening data usage are here. The white paper summarizes community guidance on the deposition and reuse of structural biology data from fragment screening, hit-to-lead, and lead-optimization studies. ⬇️Read here ⬇️ cdn.rcsb.org/wwpdb/docs/d...

cdn.rcsb.org

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 07/08/2026

🚀 Depositors can now submit structures directly to the OneDep system from the structure determination software via a newly developed Deposition API. Available now in Phenix and CCP-EM Doppio, with CCP4 and Global Phasing support coming soon. ⬇️ more ⬇️ www.wwpdb.org/news/news?ye... #PDB

wwpdb.org

New tools support deposition of structures to the wwPDB PDB and 3DEM Core Archives directly from structure determination software packages

wwPDB: Worldwide Protein Data Bank

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 06/08/2026

Out now in Journal of Applied Crystallography: mmCIF Validator, automated validation of mmCIF files against the PDBx/mmCIF dictionary Useful for structure deposition prep, biocuration, and automated QC (VS Code extension + Python/CLI) Paper: doi.org/10.1107/S160... Code: github.com/PDBeurope/mm...

doi.org

mmCIF Validator: a comprehensive validation tool for structural biology data files

The mmCIF Validator provides real-time automated validation of mmCIFs against a valid PDBx/mmCIF dictionary. The validator is available as both a Visual Studio Code extension and a standalone Python s...

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 31/07/2026

🌟 wwPDB Events at IUCr Join wwPDB members presenting at the 26th General Assembly and Congress of the International Union of Crystallography (IUCr) 🗓️ August 11-18, 2026 📍 Calgary, Canada ⬇️ More information about presentations here⬇️ www.wwpdb.org/news/news?ye...

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Reposted by Protein Data Bank in Europe (PDBe)

EMDB @emdatabank.bsky.social · 30/07/2026

Closing this weekend! Join us as a scientific biocurator in the OneDep biocuration team. Work with structural data, software and processes that support data deposition and curation. Apply by 2nd Aug: tinyurl.com/47t93kxp. CAK-CDK1-Cyclin-B1: Timing is everything (#cryoEM EMD-54971).

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 29/07/2026

🌟Save time on your next #PDB deposition with the enhanced OneDep "Based on a previous deposition" feature! This feature lets you copy and reuse metadata from a previous deposition, with ORCID support, selective import, and built-in validation. ⬇️more ⬇️ www.wwpdb.org/news/news?ye...

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Reposted by Protein Data Bank in Europe (PDBe)

EMDB @emdatabank.bsky.social · 28/07/2026

Job alert: Receptors respond to important signalling molecules (#cryoEM EMD-27634) - Our biocurators work directly with scientists to ensure their data are ready for release. Communication is key. Come join the EMDB and OneDep biocuration team. Apply by 2nd Aug: tinyurl.com/47t93kxp

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 27/07/2026

🌟 Events at Microscopy & Microanalysis Join wwPDB members for presentations on the preservation and validation of electron microscopy data at the M&M meeting. 🗓️ August 2-6, 2026 📍 Milwaukee, WI, USA. ⬇️ more ⬇️ 🔗 www.wwpdb.org/news/news?ye... 🔗 mm2026.eventscribe.net #PDB #EM

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 24/07/2026

🚨New PDBe webinar Bringing structural biology to AI: exploring the PDBe MCP servers The session will explore the capabilities offered by the PDBe MCP servers with practical examples. 🗓️ 9 September 2026 🕘 14:30-15:30 (BST) ⬇️ Register here ⬇️ www.ebi.ac.uk/training/eve... #PDB

ebi.ac.uk

Bringing structural biology to AI: exploring the PDBe MCP servers -

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Reposted by Protein Data Bank in Europe (PDBe)

EMDB @emdatabank.bsky.social · 23/07/2026

Job alert: Viruses (#cryoEM EMD-24741), chaperones, molecular assemblies, enzymes, drug targets and more. Structures tell stories. Join the EMDB and OneDep biocuration team at EMBL-EBI and help scientists tell theirs. Apply by 2nd Aug: tinyurl.com/47t93kxp

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 22/07/2026

Explore experimental and predicted macromolecular structures with PDBe tools & resources at our full-day #ECCB2026 tutorial. 📅 3 September 2026 🕘 09:00–17:30 🎤 Ibrahim Roshan & Sri Devan Appasamy 🔗 Register here: eccb2026.org/registration...

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Reposted by Protein Data Bank in Europe (PDBe)

EMDB @emdatabank.bsky.social · 21/07/2026

Job alert: Protein chaperones ensure proteins fold correctly (#cryoEM EMD-23004). Biocurators ensure structural biology data are accurate and reusable. Join the EMDB and OneDep biocurators to maintain the integrity of structural biology data. Apply by 2nd Aug: tinyurl.com/47t93kxp

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 21/07/2026

🚨 Big PDB changes are one year away Starting July 21, 2027: ▪ PDB Beta Archive becomes the main archive. ▪ Extended PDB IDs and PDBx/mmCIF will be the standard. Start using extended IDs and PDBx/mmCIF today! 🔗 www.wwpdb.org/news/news?ye... #PDB #StructuralBiology

wwpdb.org

Big PDB Changes Are One Year Away: Extended PDB IDs, the PDB Beta Archive, and PDBx/mmCIF

wwPDB: Worldwide Protein Data Bank

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Reposted by Protein Data Bank in Europe (PDBe)

EMDB @emdatabank.bsky.social · 16/07/2026

Job alert: Molecular presentation and the adaptive immune response (EMD-45166). Biocurators work closely with software devs, improving and adapting our deposition and curation pipelines. Automation is key. Come join the EMDB and OneDep biocuration team. Apply by 2nd Aug: tinyurl.com/47t93kxp

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Reposted by Protein Data Bank in Europe (PDBe)

EMDB @emdatabank.bsky.social · 14/07/2026

Job alert: Biology is amazing (EMD-70204). As a biocurator, you get a front-row seat to the structures being deposited in the world’s structural biology databases. Come join the EMDB and OneDep biocuration team. We’re hiring a biocurator. Apply by 2nd Aug: tinyurl.com/47t93kxp

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 01/07/2026

🧬 New @EMBL course: "Protein Domains: Structure, Classification & Evolution" - free & online now. CATH, SCOP, Pfam, IDRs + more. 🔗 www.ebi.ac.uk/training/onl... #StructuralBiology #Bioinformatics #Domains

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 29/06/2026

🚀 Improved support for #3DED/#MicroED is now available in the wwPDB OneDep deposition system! 🔹 New and improved metadata collection 🔹 Required structure factors for validation 🔹 SerialED metadata collection support 🔗 www.wwpdb.org/news/news?ye... #PDB #StructuralBiology

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 15/06/2026

1/2 🎬 That's a wrap on our intro to PDBe MCP Servers. All the videos are now on YouTube - install, usage, Graph Server, and Claude examples - in one playlist. 🎥 www.youtube.com/playlist?lis...

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 10/06/2026

🚀 The PDBe Graph Server is built for power users. Explore the PDBe-KB Neo4j schema with AI-assisted Cypher generation - including nodes, and edges. 🔗 Graph DB: ftp.ebi.ac.uk/pub/databases/msd/graphdb/ #Neo4j #KnowledgeGraph #PDBe #AI #Cypher

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 03/06/2026

🧬 Claude isn't the only AI that can query PDBe. PDBe MCP Servers work with other AI clients too, such as Google Antigravity. You only need one protocol for any MCP-compatible AI. 🎥 Watch the install walkthrough 👇 📦 github.com/PDBeurope/PDBe-MCP-Servers #PDBe #MCP #GoogleAntigravity #AI

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 02/06/2026

🧬 New tutorial video drop from @EMBL_EBI! "Similarity Metrics & Confidence Scores in Protein Structure Prediction" by Dr. Yonathan Goldtzvik- Essential for anyone using #AlphaFold 🎯 🎥 youtu.be/dVFHr0ZV4-0 #StructuralBiology #Bioinformatics #ProteinStructure #pLDDT

youtu.be

YouTube video by Protein Data Bank in Europe - PDBe

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Reposted by Protein Data Bank in Europe (PDBe)

EMBL-EBI @ebi.embl.org · 28/05/2026

We told you it wouldn’t be a long wait. 👀 Even more predicted protein structures have been added to the #AlphaFold Database. This time, the database has expanded to include heterodimers – protein complexes made up of two different proteins. alphafold.ebi.ac.uk

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 27/05/2026

Connect Claude to PDBe in 3 steps: 1️⃣ Install uv 2️⃣ Run: uvx pdbe-mcp-server --server-type pdbe_api_server 3️⃣ Add config to Claude Desktop Now ask: “Find X-ray structures for UniProt P12345” 📦 github.com/PDBeurope/PDBe-MCP-Servers #PDBe #MCP #ClaudeAI #Bioinformatics

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 22/05/2026

What’s inside the PDBe MCP package? ⚡ API Server Live structural biology data via REST-powered MCP tools 🔍 Search Server Schema-aware Solr search across PDBe 🌐 Graph Server Neo4j schema exploration + Cypher generation One install. Three servers. Unlimited workflows. #PDBe #MCP #Bioinformatics

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 20/05/2026

6/6 Built at @EBI_EMBL by Sreenath Sasidharan Nair 💙 Apache 2.0 · Python 3.10+ We’d love to see what the community builds next. #PDBe #MCP #ModelContextProtocol #StructuralBiology #AI

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 20/05/2026

5/6 What can you build with it? → Ask Claude about any PDB entry in plain English. → Generate Cypher queries with schema awareness. → Build structural biology copilots. → Create lab assistants powered by live PDBe data. → Explore protein structure graphs interactively.

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 20/05/2026

4/6 Get started in under a minute: uvx pdbe-mcp-server Works with Claude Desktop on macOS, Windows, and Linux. 📦 PyPI: pypi.org/project/pdbe-mcp-server 💻 GitHub: github.com/PDBeurope/PDBe-MCP-Servers

pypi.org

Client Challenge

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 20/05/2026

3/6 PDBe MCP Servers provide AI access to: ⚡ API Server — biological structure data via REST 🔍 Search Server — Solr-powered schema-aware search 🌐 Graph Server — Neo4j schema + Cypher query generation One protocol. Three servers. Infinite possibilities.

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 20/05/2026

2/6 LLMs can describe protein structures. But until now, they couldn’t actually access PDBe’s live data. No fresh depositions. No schema-aware search. No graph exploration. No structured retrieval. So we built the bridge.

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 20/05/2026

1/6 🧪 Big news for structural biology and AI: PDBe is now AI-native. We’ve built MCP Servers that connect the Protein Data Bank in Europe and the Alphafold Protein Structure Database directly to Claude and other MCP-compatible AI systems. Here’s what that unlocks 👇

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 14/05/2026

PDBe-SIFTS is now open source 🎉 Developed in collaboration with PDBe (@pdbeurope.bsky.social) and UniProt, it enables fast, accurate residue-level mapping between protein sequences and structures, achieving >93% agreement with curated mappings. Get started: github.com/PDBeurope/SI...

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 08/05/2026

Our new bioRxiv preprint introduces ECIFP: a scalable interaction fingerprint that maps the landscape of ligand binding modes. ✅Identified binding modes for 9k+ ligands ✅Analysis of 48k+ binding sites from 21k+ proteins ✅Open-source & interpretable ⬇️ more ⬇️ www.biorxiv.org/content/10.6... #PDB

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 01/05/2026

🚨𝗡𝗲𝘄 𝗦𝘆𝗻𝘁𝗮𝘅 𝗳𝗼𝗿 𝗣𝗗𝗕 𝗗𝗢𝗜𝘀 𝗳𝗼𝗿 𝗘𝗻𝘁𝗿𝗶𝗲𝘀 𝗥𝗲𝗹𝗲𝗮𝘀𝗲𝗱 𝗔𝗳𝘁𝗲𝗿 𝗝𝘂𝗹𝘆 𝟮𝟭, 𝟮𝟬𝟮𝟳 • New entries DOI will use extended ID (e.g. 10.2210/pdb_1000axyz/pdb) • Older entries keep 4-character DOI format (e.g. 10.2210/pdb1abc/pdb) 🔗https://www.wwpdb.org/news/news?year=2026#69ebcf461103c56d3f44415a #PDB

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